A new and efficient method for overcoming the multiple minima ## Ε½ . problem of polypeptides, the systematic stepsize variation SSV method, is presented. The SSV is based on the assumption that energy barriers can be passed over by sufficiently large rotations about rotatable bonds: randomly Ε½ cho
An unbounded systematic search of conformational space
β Scribed by Jonathan M. Goodman; W. Clark Still
- Book ID
- 102879561
- Publisher
- John Wiley and Sons
- Year
- 1991
- Tongue
- English
- Weight
- 790 KB
- Volume
- 12
- Category
- Article
- ISSN
- 0192-8651
No coin nor oath required. For personal study only.
β¦ Synopsis
A new method for searching internal coordinate conformational space systematically via a continuous-process procedure is described. Unlike previous systematic search methods, the new scheme generates torsionally remote conformers early in the search. It is also unbounded in that the extent of the search need not be specified at the outset. The search begins at low resolution (120" in torsion angle space) and then goes to higher and higher resolution as all points in space at a given resolution have been searched. The search may run without end or be terminated when new conformers cease to be found or when all space at some maximum allowable resolution has been explored. Conformational searches on several medium-and large-ring molecules using the new method are described and the results are compared with those from certain previously described search methods. It is found that the new method is significantly more efficient than previous procedures at finding all low energy conformers of organic molecules.
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## Abstract The present study involves the utilization of replica exchange molecular dynamics (REMD) methodology to explore the conformational space of Neuromedin C (NMC) using implicit (REMD^implicit^) and explicit (REMD^explicit^) water models. Comparison of the structures obtained from these sim
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